5LIG | pdb_00005lig

G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2

• PDB DOI: https://doi.org/10.2210/pdb5LIG/pdb
• BMRB: 34025
• NAKB: 5LIG

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-07-14 Released: 2016-09-14 
• Deposition Author(s): Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.

Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.

(2016) Angew Chem Int Ed Engl 55: 12508-12511

• PubMed: 27577037 
• DOI: https://doi.org/10.1002/anie.201606877
• Primary Citation Related Structures: 
  5LIG


• PubMed Abstract: 
  

  An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.

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Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK.
Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. [e-mail].
EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. [e-mail].
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia. [e-mail].

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.09 kDa 
• Atom Count: 481 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	A	19	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6XM	B [auth A], C [auth A]	8,12-bis(2-morpholinoethyl)-8H-benzo[ij]xantheno[1,9,8-cdef][2,7]naphthyridin-12-iumhexafluorophosphate C31 H34 N4 O3 JDODSALIMITEDK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-242
Slovenian Research Agency	Slovenia	J1-6733

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2018-02-14
  Changes: Data collection
• Version 2.0: 2018-03-07
  Changes: Advisory, Atomic model, Derived calculations, Non-polymer description
• Version 2.1: 2019-05-08
  Changes: Data collection
• Version 2.2: 2024-05-15
  Changes: Data collection, Database references